diff --git a/nanobot/cli/commands.py b/nanobot/cli/commands.py
index 87b2bc5..2773323 100644
--- a/nanobot/cli/commands.py
+++ b/nanobot/cli/commands.py
@@ -34,7 +34,7 @@ from rich.text import Text
 
 from nanobot import __logo__, __version__
 from nanobot.cli.stream import StreamRenderer, ThinkingSpinner
-from nanobot.config.paths import get_workspace_path
+from nanobot.config.paths import get_workspace_path, is_default_workspace
 from nanobot.config.schema import Config
 from nanobot.utils.helpers import sync_workspace_templates
 
@@ -479,6 +479,17 @@ def _warn_deprecated_config_keys(config_path: Path | None) -> None:
         )
 
 
+def _migrate_cron_store(config: "Config") -> None:
+    """One-time migration: move legacy global cron store into the workspace."""
+    from nanobot.config.paths import get_cron_dir
+
+    legacy_path = get_cron_dir() / "jobs.json"
+    new_path = config.workspace_path / "cron" / "jobs.json"
+    if legacy_path.is_file() and not new_path.exists():
+        new_path.parent.mkdir(parents=True, exist_ok=True)
+        import shutil
+        shutil.move(str(legacy_path), str(new_path))
+
 
 # ============================================================================
 # Gateway / Server
@@ -496,7 +507,6 @@ def gateway(
     from nanobot.agent.loop import AgentLoop
     from nanobot.bus.queue import MessageBus
     from nanobot.channels.manager import ChannelManager
-    from nanobot.config.paths import get_cron_dir
     from nanobot.cron.service import CronService
     from nanobot.cron.types import CronJob
     from nanobot.heartbeat.service import HeartbeatService
@@ -515,8 +525,12 @@ def gateway(
     provider = _make_provider(config)
     session_manager = SessionManager(config.workspace_path)
 
-    # Create cron service first (callback set after agent creation)
-    cron_store_path = get_cron_dir() / "jobs.json"
+    # Preserve existing single-workspace installs, but keep custom workspaces clean.
+    if is_default_workspace(config.workspace_path):
+        _migrate_cron_store(config)
+
+    # Create cron service with workspace-scoped store
+    cron_store_path = config.workspace_path / "cron" / "jobs.json"
     cron = CronService(cron_store_path)
 
     # Create agent with cron service
@@ -703,7 +717,6 @@ def agent(
 
     from nanobot.agent.loop import AgentLoop
     from nanobot.bus.queue import MessageBus
-    from nanobot.config.paths import get_cron_dir
     from nanobot.cron.service import CronService
 
     config = _load_runtime_config(config, workspace)
@@ -712,8 +725,12 @@ def agent(
     bus = MessageBus()
     provider = _make_provider(config)
 
-    # Create cron service for tool usage (no callback needed for CLI unless running)
-    cron_store_path = get_cron_dir() / "jobs.json"
+    # Preserve existing single-workspace installs, but keep custom workspaces clean.
+    if is_default_workspace(config.workspace_path):
+        _migrate_cron_store(config)
+
+    # Create cron service with workspace-scoped store
+    cron_store_path = config.workspace_path / "cron" / "jobs.json"
     cron = CronService(cron_store_path)
 
     if logs:
diff --git a/nanobot/config/__init__.py b/nanobot/config/__init__.py
index e2c24f8..4b9fcce 100644
--- a/nanobot/config/__init__.py
+++ b/nanobot/config/__init__.py
@@ -7,6 +7,7 @@ from nanobot.config.paths import (
     get_cron_dir,
     get_data_dir,
     get_legacy_sessions_dir,
+    is_default_workspace,
     get_logs_dir,
     get_media_dir,
     get_runtime_subdir,
@@ -24,6 +25,7 @@ __all__ = [
     "get_cron_dir",
     "get_logs_dir",
     "get_workspace_path",
+    "is_default_workspace",
     "get_cli_history_path",
     "get_bridge_install_dir",
     "get_legacy_sessions_dir",
diff --git a/nanobot/config/paths.py b/nanobot/config/paths.py
index f4dfbd9..527c5f3 100644
--- a/nanobot/config/paths.py
+++ b/nanobot/config/paths.py
@@ -40,6 +40,13 @@ def get_workspace_path(workspace: str | None = None) -> Path:
     return ensure_dir(path)
 
 
+def is_default_workspace(workspace: str | Path | None) -> bool:
+    """Return whether a workspace resolves to nanobot's default workspace path."""
+    current = Path(workspace).expanduser() if workspace is not None else Path.home() / ".nanobot" / "workspace"
+    default = Path.home() / ".nanobot" / "workspace"
+    return current.resolve(strict=False) == default.resolve(strict=False)
+
+
 def get_cli_history_path() -> Path:
     """Return the shared CLI history file path."""
     return Path.home() / ".nanobot" / "history" / "cli_history"
diff --git a/tests/test_commands.py b/tests/test_commands.py
index 5d4c2bc..68cc429 100644
--- a/tests/test_commands.py
+++ b/tests/test_commands.py
@@ -333,10 +333,8 @@ def mock_agent_runtime(tmp_path):
     """Mock agent command dependencies for focused CLI tests."""
     config = Config()
     config.agents.defaults.workspace = str(tmp_path / "default-workspace")
-    cron_dir = tmp_path / "data" / "cron"
 
     with patch("nanobot.config.loader.load_config", return_value=config) as mock_load_config, \
-         patch("nanobot.config.paths.get_cron_dir", return_value=cron_dir), \
          patch("nanobot.cli.commands.sync_workspace_templates") as mock_sync_templates, \
          patch("nanobot.cli.commands._make_provider", return_value=object()), \
          patch("nanobot.cli.commands._print_agent_response") as mock_print_response, \
@@ -413,7 +411,6 @@ def test_agent_config_sets_active_path(monkeypatch, tmp_path: Path) -> None:
         lambda path: seen.__setitem__("config_path", path),
     )
     monkeypatch.setattr("nanobot.config.loader.load_config", lambda _path=None: config)
-    monkeypatch.setattr("nanobot.config.paths.get_cron_dir", lambda: config_file.parent / "cron")
     monkeypatch.setattr("nanobot.cli.commands.sync_workspace_templates", lambda _path: None)
     monkeypatch.setattr("nanobot.cli.commands._make_provider", lambda _config: object())
     monkeypatch.setattr("nanobot.bus.queue.MessageBus", lambda: object())
@@ -438,6 +435,147 @@ def test_agent_config_sets_active_path(monkeypatch, tmp_path: Path) -> None:
     assert seen["config_path"] == config_file.resolve()
 
 
+def test_agent_uses_workspace_directory_for_cron_store(monkeypatch, tmp_path: Path) -> None:
+    config_file = tmp_path / "instance" / "config.json"
+    config_file.parent.mkdir(parents=True)
+    config_file.write_text("{}")
+
+    config = Config()
+    config.agents.defaults.workspace = str(tmp_path / "agent-workspace")
+    seen: dict[str, Path] = {}
+
+    monkeypatch.setattr("nanobot.config.loader.set_config_path", lambda _path: None)
+    monkeypatch.setattr("nanobot.config.loader.load_config", lambda _path=None: config)
+    monkeypatch.setattr("nanobot.cli.commands.sync_workspace_templates", lambda _path: None)
+    monkeypatch.setattr("nanobot.cli.commands._make_provider", lambda _config: object())
+    monkeypatch.setattr("nanobot.bus.queue.MessageBus", lambda: object())
+
+    class _FakeCron:
+        def __init__(self, store_path: Path) -> None:
+            seen["cron_store"] = store_path
+
+    class _FakeAgentLoop:
+        def __init__(self, *args, **kwargs) -> None:
+            pass
+
+        async def process_direct(self, *_args, **_kwargs):
+            return OutboundMessage(channel="cli", chat_id="direct", content="ok")
+
+        async def close_mcp(self) -> None:
+            return None
+
+    monkeypatch.setattr("nanobot.cron.service.CronService", _FakeCron)
+    monkeypatch.setattr("nanobot.agent.loop.AgentLoop", _FakeAgentLoop)
+    monkeypatch.setattr("nanobot.cli.commands._print_agent_response", lambda *_args, **_kwargs: None)
+
+    result = runner.invoke(app, ["agent", "-m", "hello", "-c", str(config_file)])
+
+    assert result.exit_code == 0
+    assert seen["cron_store"] == config.workspace_path / "cron" / "jobs.json"
+
+
+def test_agent_workspace_override_does_not_migrate_legacy_cron(
+    monkeypatch, tmp_path: Path
+) -> None:
+    config_file = tmp_path / "instance" / "config.json"
+    config_file.parent.mkdir(parents=True)
+    config_file.write_text("{}")
+
+    legacy_dir = tmp_path / "global" / "cron"
+    legacy_dir.mkdir(parents=True)
+    legacy_file = legacy_dir / "jobs.json"
+    legacy_file.write_text('{"jobs": []}')
+
+    override = tmp_path / "override-workspace"
+    config = Config()
+    seen: dict[str, Path] = {}
+
+    monkeypatch.setattr("nanobot.config.loader.set_config_path", lambda _path: None)
+    monkeypatch.setattr("nanobot.config.loader.load_config", lambda _path=None: config)
+    monkeypatch.setattr("nanobot.cli.commands.sync_workspace_templates", lambda _path: None)
+    monkeypatch.setattr("nanobot.cli.commands._make_provider", lambda _config: object())
+    monkeypatch.setattr("nanobot.bus.queue.MessageBus", lambda: object())
+    monkeypatch.setattr("nanobot.config.paths.get_cron_dir", lambda: legacy_dir)
+
+    class _FakeCron:
+        def __init__(self, store_path: Path) -> None:
+            seen["cron_store"] = store_path
+
+    class _FakeAgentLoop:
+        def __init__(self, *args, **kwargs) -> None:
+            pass
+
+        async def process_direct(self, *_args, **_kwargs):
+            return OutboundMessage(channel="cli", chat_id="direct", content="ok")
+
+        async def close_mcp(self) -> None:
+            return None
+
+    monkeypatch.setattr("nanobot.cron.service.CronService", _FakeCron)
+    monkeypatch.setattr("nanobot.agent.loop.AgentLoop", _FakeAgentLoop)
+    monkeypatch.setattr("nanobot.cli.commands._print_agent_response", lambda *_args, **_kwargs: None)
+
+    result = runner.invoke(
+        app,
+        ["agent", "-m", "hello", "-c", str(config_file), "-w", str(override)],
+    )
+
+    assert result.exit_code == 0
+    assert seen["cron_store"] == override / "cron" / "jobs.json"
+    assert legacy_file.exists()
+    assert not (override / "cron" / "jobs.json").exists()
+
+
+def test_agent_custom_config_workspace_does_not_migrate_legacy_cron(
+    monkeypatch, tmp_path: Path
+) -> None:
+    config_file = tmp_path / "instance" / "config.json"
+    config_file.parent.mkdir(parents=True)
+    config_file.write_text("{}")
+
+    legacy_dir = tmp_path / "global" / "cron"
+    legacy_dir.mkdir(parents=True)
+    legacy_file = legacy_dir / "jobs.json"
+    legacy_file.write_text('{"jobs": []}')
+
+    custom_workspace = tmp_path / "custom-workspace"
+    config = Config()
+    config.agents.defaults.workspace = str(custom_workspace)
+    seen: dict[str, Path] = {}
+
+    monkeypatch.setattr("nanobot.config.loader.set_config_path", lambda _path: None)
+    monkeypatch.setattr("nanobot.config.loader.load_config", lambda _path=None: config)
+    monkeypatch.setattr("nanobot.cli.commands.sync_workspace_templates", lambda _path: None)
+    monkeypatch.setattr("nanobot.cli.commands._make_provider", lambda _config: object())
+    monkeypatch.setattr("nanobot.bus.queue.MessageBus", lambda: object())
+    monkeypatch.setattr("nanobot.config.paths.get_cron_dir", lambda: legacy_dir)
+
+    class _FakeCron:
+        def __init__(self, store_path: Path) -> None:
+            seen["cron_store"] = store_path
+
+    class _FakeAgentLoop:
+        def __init__(self, *args, **kwargs) -> None:
+            pass
+
+        async def process_direct(self, *_args, **_kwargs):
+            return OutboundMessage(channel="cli", chat_id="direct", content="ok")
+
+        async def close_mcp(self) -> None:
+            return None
+
+    monkeypatch.setattr("nanobot.cron.service.CronService", _FakeCron)
+    monkeypatch.setattr("nanobot.agent.loop.AgentLoop", _FakeAgentLoop)
+    monkeypatch.setattr("nanobot.cli.commands._print_agent_response", lambda *_args, **_kwargs: None)
+
+    result = runner.invoke(app, ["agent", "-m", "hello", "-c", str(config_file)])
+
+    assert result.exit_code == 0
+    assert seen["cron_store"] == custom_workspace / "cron" / "jobs.json"
+    assert legacy_file.exists()
+    assert not (custom_workspace / "cron" / "jobs.json").exists()
+
+
 def test_agent_overrides_workspace_path(mock_agent_runtime):
     workspace_path = Path("/tmp/agent-workspace")
 
@@ -544,7 +682,7 @@ def test_gateway_workspace_option_overrides_config(monkeypatch, tmp_path: Path)
     assert config.workspace_path == override
 
 
-def test_gateway_uses_config_directory_for_cron_store(monkeypatch, tmp_path: Path) -> None:
+def test_gateway_uses_workspace_directory_for_cron_store(monkeypatch, tmp_path: Path) -> None:
     config_file = tmp_path / "instance" / "config.json"
     config_file.parent.mkdir(parents=True)
     config_file.write_text("{}")
@@ -555,7 +693,6 @@ def test_gateway_uses_config_directory_for_cron_store(monkeypatch, tmp_path: Pat
 
     monkeypatch.setattr("nanobot.config.loader.set_config_path", lambda _path: None)
     monkeypatch.setattr("nanobot.config.loader.load_config", lambda _path=None: config)
-    monkeypatch.setattr("nanobot.config.paths.get_cron_dir", lambda: config_file.parent / "cron")
     monkeypatch.setattr("nanobot.cli.commands.sync_workspace_templates", lambda _path: None)
     monkeypatch.setattr("nanobot.cli.commands._make_provider", lambda _config: object())
     monkeypatch.setattr("nanobot.bus.queue.MessageBus", lambda: object())
@@ -571,7 +708,130 @@ def test_gateway_uses_config_directory_for_cron_store(monkeypatch, tmp_path: Pat
     result = runner.invoke(app, ["gateway", "--config", str(config_file)])
 
     assert isinstance(result.exception, _StopGatewayError)
-    assert seen["cron_store"] == config_file.parent / "cron" / "jobs.json"
+    assert seen["cron_store"] == config.workspace_path / "cron" / "jobs.json"
+
+
+def test_gateway_workspace_override_does_not_migrate_legacy_cron(
+    monkeypatch, tmp_path: Path
+) -> None:
+    config_file = tmp_path / "instance" / "config.json"
+    config_file.parent.mkdir(parents=True)
+    config_file.write_text("{}")
+
+    legacy_dir = tmp_path / "global" / "cron"
+    legacy_dir.mkdir(parents=True)
+    legacy_file = legacy_dir / "jobs.json"
+    legacy_file.write_text('{"jobs": []}')
+
+    override = tmp_path / "override-workspace"
+    config = Config()
+    seen: dict[str, Path] = {}
+
+    monkeypatch.setattr("nanobot.config.loader.set_config_path", lambda _path: None)
+    monkeypatch.setattr("nanobot.config.loader.load_config", lambda _path=None: config)
+    monkeypatch.setattr("nanobot.cli.commands.sync_workspace_templates", lambda _path: None)
+    monkeypatch.setattr("nanobot.cli.commands._make_provider", lambda _config: object())
+    monkeypatch.setattr("nanobot.bus.queue.MessageBus", lambda: object())
+    monkeypatch.setattr("nanobot.session.manager.SessionManager", lambda _workspace: object())
+    monkeypatch.setattr("nanobot.config.paths.get_cron_dir", lambda: legacy_dir)
+
+    class _StopCron:
+        def __init__(self, store_path: Path) -> None:
+            seen["cron_store"] = store_path
+            raise _StopGatewayError("stop")
+
+    monkeypatch.setattr("nanobot.cron.service.CronService", _StopCron)
+
+    result = runner.invoke(
+        app,
+        ["gateway", "--config", str(config_file), "--workspace", str(override)],
+    )
+
+    assert isinstance(result.exception, _StopGatewayError)
+    assert seen["cron_store"] == override / "cron" / "jobs.json"
+    assert legacy_file.exists()
+    assert not (override / "cron" / "jobs.json").exists()
+
+
+def test_gateway_custom_config_workspace_does_not_migrate_legacy_cron(
+    monkeypatch, tmp_path: Path
+) -> None:
+    config_file = tmp_path / "instance" / "config.json"
+    config_file.parent.mkdir(parents=True)
+    config_file.write_text("{}")
+
+    legacy_dir = tmp_path / "global" / "cron"
+    legacy_dir.mkdir(parents=True)
+    legacy_file = legacy_dir / "jobs.json"
+    legacy_file.write_text('{"jobs": []}')
+
+    custom_workspace = tmp_path / "custom-workspace"
+    config = Config()
+    config.agents.defaults.workspace = str(custom_workspace)
+    seen: dict[str, Path] = {}
+
+    monkeypatch.setattr("nanobot.config.loader.set_config_path", lambda _path: None)
+    monkeypatch.setattr("nanobot.config.loader.load_config", lambda _path=None: config)
+    monkeypatch.setattr("nanobot.cli.commands.sync_workspace_templates", lambda _path: None)
+    monkeypatch.setattr("nanobot.cli.commands._make_provider", lambda _config: object())
+    monkeypatch.setattr("nanobot.bus.queue.MessageBus", lambda: object())
+    monkeypatch.setattr("nanobot.session.manager.SessionManager", lambda _workspace: object())
+    monkeypatch.setattr("nanobot.config.paths.get_cron_dir", lambda: legacy_dir)
+
+    class _StopCron:
+        def __init__(self, store_path: Path) -> None:
+            seen["cron_store"] = store_path
+            raise _StopGatewayError("stop")
+
+    monkeypatch.setattr("nanobot.cron.service.CronService", _StopCron)
+
+    result = runner.invoke(app, ["gateway", "--config", str(config_file)])
+
+    assert isinstance(result.exception, _StopGatewayError)
+    assert seen["cron_store"] == custom_workspace / "cron" / "jobs.json"
+    assert legacy_file.exists()
+    assert not (custom_workspace / "cron" / "jobs.json").exists()
+
+
+def test_migrate_cron_store_moves_legacy_file(tmp_path: Path) -> None:
+    """Legacy global jobs.json is moved into the workspace on first run."""
+    from nanobot.cli.commands import _migrate_cron_store
+
+    legacy_dir = tmp_path / "global" / "cron"
+    legacy_dir.mkdir(parents=True)
+    legacy_file = legacy_dir / "jobs.json"
+    legacy_file.write_text('{"jobs": []}')
+
+    config = Config()
+    config.agents.defaults.workspace = str(tmp_path / "workspace")
+    workspace_cron = config.workspace_path / "cron" / "jobs.json"
+
+    with patch("nanobot.config.paths.get_cron_dir", return_value=legacy_dir):
+        _migrate_cron_store(config)
+
+    assert workspace_cron.exists()
+    assert workspace_cron.read_text() == '{"jobs": []}'
+    assert not legacy_file.exists()
+
+
+def test_migrate_cron_store_skips_when_workspace_file_exists(tmp_path: Path) -> None:
+    """Migration does not overwrite an existing workspace cron store."""
+    from nanobot.cli.commands import _migrate_cron_store
+
+    legacy_dir = tmp_path / "global" / "cron"
+    legacy_dir.mkdir(parents=True)
+    (legacy_dir / "jobs.json").write_text('{"old": true}')
+
+    config = Config()
+    config.agents.defaults.workspace = str(tmp_path / "workspace")
+    workspace_cron = config.workspace_path / "cron" / "jobs.json"
+    workspace_cron.parent.mkdir(parents=True)
+    workspace_cron.write_text('{"new": true}')
+
+    with patch("nanobot.config.paths.get_cron_dir", return_value=legacy_dir):
+        _migrate_cron_store(config)
+
+    assert workspace_cron.read_text() == '{"new": true}'
 
 
 def test_gateway_uses_configured_port_when_cli_flag_is_missing(monkeypatch, tmp_path: Path) -> None:
diff --git a/tests/test_config_paths.py b/tests/test_config_paths.py
index 473a6c8..6c560ce 100644
--- a/tests/test_config_paths.py
+++ b/tests/test_config_paths.py
@@ -10,6 +10,7 @@ from nanobot.config.paths import (
     get_media_dir,
     get_runtime_subdir,
     get_workspace_path,
+    is_default_workspace,
 )
 
 
@@ -40,3 +41,9 @@ def test_shared_and_legacy_paths_remain_global() -> None:
 def test_workspace_path_is_explicitly_resolved() -> None:
     assert get_workspace_path() == Path.home() / ".nanobot" / "workspace"
     assert get_workspace_path("~/custom-workspace") == Path.home() / "custom-workspace"
+
+
+def test_is_default_workspace_distinguishes_default_and_custom_paths() -> None:
+    assert is_default_workspace(None) is True
+    assert is_default_workspace(Path.home() / ".nanobot" / "workspace") is True
+    assert is_default_workspace("~/custom-workspace") is False